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(-) Description

Title :  BENCE JONES PROTEIN CLE, A LAMBDA III IMMUNOGLOBULIN LIGHT-CHAIN DIMER
 
Authors :  M. Schiffer, D. B. Huang
Date :  13 May 96  (Deposition) - 15 May 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Immunoglobulin, Bence Jones Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. B. Huang, C. Ainsworth, A. Solomon, M. Schiffer
Pitfalls Of Molecular Replacement: The Structure Determination Of An Immunoglobulin Light-Chain Dimer.
Acta Crystallogr. , Sect. D V. 52 1058 1996
PubMed-ID: 15299564  |  Reference-DOI: 10.1107/S090744499600813X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LAMBDA III BENCE JONES PROTEIN CLE
    ChainsA, B
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1LIL)

(-) Sites  (0, 0)

(no "Site" information available for 1LIL)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3A:214 -B:214
4B:23 -B:88
5B:134 -B:194

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:140 -Pro A:141
2Tyr B:140 -Pro B:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LIL)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.IGLC1_HUMAN85-91
 
  2A:192-198
B:192-198
IGLC2_HUMAN85-91
 
  2A:192-198
B:192-198

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003903231ENSE00001721671chr22:23243156-23243617462IGLC2_HUMAN1-1061062A:107-215 (gaps)
B:107-215 (gaps)
109
109

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:212
 aligned with IGLC1_HUMAN | P0CG04 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:212
                                                                                                                                      1                                                                                                         
                                     -         -         -         -         -         -         -         -         -         -      |  4        14        24        34        44        54        64        74        84        94       104  
         IGLC1_HUMAN      - ----------------------------------------------------------------------------------------------------------GQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS  106
               SCOP domains d1lila1 A:2-107 Immunoglobulin light chain lambda variable domain, VL-lambda                               d1lila2 A:108-215 Immunoglobulin light chain lambda constant domain, CL-lambda                            SCOP domains
               CATH domains 1lilA01 A:2-107 Immunoglobulins                                                                            1lilA02 A:108-211 Immunoglobulins                                                                    ---- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeeee.......eeeeeeee......eeee.............eeeeee..eeeeee....hhh..eeeeeeee...eeee....eeee........eeeee...hhhhh....eeeeeee........eeeee.......................eeeeee..hhhhhh...eeeee................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lil A    2 YEVTQPPSLSVSPGQTARITCSGEKLGDAYVCWYQQRPGQSPVVVIYQDNRRPSGIPERFSGSSSGNTATLTISGTQTLDEADYYCQVWDSNASVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS  215
                                   |12        22        32        42        52        62        72        82        92   |   101     | 110       120       130       140       150       160       171       181       191       203       213  
                                   9|                                                                                  95A        106A                                                           168|                           200|            
                                   11                                                                                                                                                             170                            203            

Chain A from PDB  Type:PROTEIN  Length:212
 aligned with IGLC2_HUMAN | P0DOY2 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:212
                                                                                                                                      1                                                                                                         
                                     -         -         -         -         -         -         -         -         -         -      |  4        14        24        34        44        54        64        74        84        94       104  
         IGLC2_HUMAN      - ----------------------------------------------------------------------------------------------------------GQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS  106
               SCOP domains d1lila1 A:2-107 Immunoglobulin light chain lambda variable domain, VL-lambda                               d1lila2 A:108-215 Immunoglobulin light chain lambda constant domain, CL-lambda                            SCOP domains
               CATH domains 1lilA01 A:2-107 Immunoglobulins                                                                            1lilA02 A:108-211 Immunoglobulins                                                                    ---- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeeee.......eeeeeeee......eeee.............eeeeee..eeeeee....hhh..eeeeeeee...eeee....eeee........eeeee...hhhhh....eeeeeee........eeeee.......................eeeeee..hhhhhh...eeeee................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
               Transcript 1 ----------------------------------------------------------------------------------------------------------Exon 1.1  PDB: A:107-215 (gaps) UniProt: 1-106                                                             Transcript 1
                1lil A    2 YEVTQPPSLSVSPGQTARITCSGEKLGDAYVCWYQQRPGQSPVVVIYQDNRRPSGIPERFSGSSSGNTATLTISGTQTLDEADYYCQVWDSNASVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS  215
                                   |12        22        32        42        52        62        72        82        92   |   101     | 110       120       130       140       150       160       171       181       191       203       213  
                                   9|                                                                                  95A        106A                                                           168|                           200|            
                                   11                                                                                                                                                             170                            203            

Chain B from PDB  Type:PROTEIN  Length:212
 aligned with IGLC1_HUMAN | P0CG04 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:212
                                                                                                                                      1                                                                                                         
                                     -         -         -         -         -         -         -         -         -         -      |  4        14        24        34        44        54        64        74        84        94       104  
         IGLC1_HUMAN      - ----------------------------------------------------------------------------------------------------------GQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS  106
               SCOP domains d1lilb1 B:2-107 Immunoglobulin light chain lambda variable domain, VL-lambda                               d1lilb2 B:108-215 Immunoglobulin light chain lambda constant domain, CL-lambda                            SCOP domains
               CATH domains 1lilB01 B:2-107 Immunoglobulins                                                                            1lilB02 B:108-211 Immunoglobulins                                                                    ---- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...eeeeeee...hhheeeeeeee......eeee.............eeeee...eeeeeee.......eeeeeeeee....eee...eeeeee.......eeeee...hhhhhh..eeeeeeee.......eeeeee........eee...........eeeeeeee.hhhh.....eeeeee....eeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lil B    2 YEVTQPPSLSVSPGQTARITCSGEKLGDAYVCWYQQRPGQSPVVVIYQDNRRPSGIPERFSGSSSGNTATLTISGTQTLDEADYYCQVWDSNASVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS  215
                                   |12        22        32        42        52        62        72        82        92   |   101     | 110       120       130       140       150       160       171       181       191       203       213  
                                   9|                                                                                  95A        106A                                                           168|                           200|            
                                   11                                                                                                                                                             170                            203            

Chain B from PDB  Type:PROTEIN  Length:212
 aligned with IGLC2_HUMAN | P0DOY2 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:212
                                                                                                                                      1                                                                                                         
                                     -         -         -         -         -         -         -         -         -         -      |  4        14        24        34        44        54        64        74        84        94       104  
         IGLC2_HUMAN      - ----------------------------------------------------------------------------------------------------------GQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS  106
               SCOP domains d1lilb1 B:2-107 Immunoglobulin light chain lambda variable domain, VL-lambda                               d1lilb2 B:108-215 Immunoglobulin light chain lambda constant domain, CL-lambda                            SCOP domains
               CATH domains 1lilB01 B:2-107 Immunoglobulins                                                                            1lilB02 B:108-211 Immunoglobulins                                                                    ---- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...eeeeeee...hhheeeeeeee......eeee.............eeeee...eeeeeee.......eeeeeeeee....eee...eeeeee.......eeeee...hhhhhh..eeeeeeee.......eeeeee........eee...........eeeeeeee.hhhh.....eeeeee....eeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
               Transcript 1 ----------------------------------------------------------------------------------------------------------Exon 1.1  PDB: B:107-215 (gaps) UniProt: 1-106                                                             Transcript 1
                1lil B    2 YEVTQPPSLSVSPGQTARITCSGEKLGDAYVCWYQQRPGQSPVVVIYQDNRRPSGIPERFSGSSSGNTATLTISGTQTLDEADYYCQVWDSNASVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS  215
                                   |12        22        32        42        52        62        72        82        92   |   101     | 110       120       130       140       150       160       171       181       191       203       213  
                                   9|                                                                                  95A        106A                                                           168|                           200|            
                                   11                                                                                                                                                             170                            203            

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1LIL)

(-) Gene Ontology  (24, 47)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (IGLC1_HUMAN | P0CG04)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
    GO:0034987    immunoglobulin receptor binding    Interacting selectively and non-covalently with one or more specific sites on an immunoglobulin receptor molecule.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0050853    B cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
    GO:0038095    Fc-epsilon receptor signaling pathway    A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
    GO:0038096    Fc-gamma receptor signaling pathway involved in phagocytosis    An Fc-gamma receptor signaling pathway that contributes to the endocytic engulfment of external particulate material by phagocytes.
    GO:0006956    complement activation    Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway.
    GO:0006958    complement activation, classical pathway    Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0006911    phagocytosis, engulfment    The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis.
    GO:0006910    phagocytosis, recognition    The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.
    GO:0050871    positive regulation of B cell activation    Any process that activates or increases the frequency, rate or extent of B cell activation.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
cellular component
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0042571    immunoglobulin complex, circulating    An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A,B   (IGLC2_HUMAN | P0DOY2)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        IGLC1_HUMAN | P0CG041aqk 1zvo 2fb4 2ig2
        IGLC2_HUMAN | P0DOY21jvk 1zvo 2jb5 2jb6 3c2a 3tv3 3twc 3tyg 4eow 4lld 4llm 4llq 4llu 4llw 4lly 4o58 4o5i 5d9q 5iq7 5iq9

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1LIL)